Lin, who along with Algerian boxer Imane Khelif was embroiled in a gender row at the Paris Olympics, was due to compete in the World Boxing Cup Finals in Sheffield starting Wednesday.
The new competition was organised by World Boxing, which was founded in 2023 and boasts around 55 members, including Taiwan.
It was to be Lin's first international competition since Paris, but she withdrew after World Boxing questioned her eligibility, Taiwan's Sports Administration said in a statement.
"She is female, meets all eligibility criteria, and successfully participated in the women's boxing event (in Paris), winning a gold medal," the statement said.
"Unfortunately, as World Boxing is newly established and still navigating the development of its operational mechanisms, it lacks the clear regulatory policies of the IOC that ensure the protection of athletes' rights," it said, referring to the International Olympic Committee.
"Additionally, World Boxing's medical committee has yet to establish robust confidentiality procedures to safeguard the medical information submitted by Taiwan regarding Lin Yu-ting."
Lin had offered to undergo a "comprehensive medical examination locally" in Britain but World Boxing did not agree, the statement said.
To avoid further "harm" to Lin, her coach and Taiwanese sports officials "decided to withdraw from this event proactively".
Lin had arrived in Britain a few days ago and pulled out of the event on Tuesday, Hsieh Chi-ying from the Sports Administration told AFP.
Neither World Boxing nor England Boxing immediately responded to AFP's requests for comment.
Lin and Khelif were thrown out of last year's world championships -- which was run by the Russian-led International Boxing Association (IBA)-- but they were cleared by the IOC to compete in Paris.
IBA's Kremlin-linked president Umar Kremlev claimed in a chaotic press conference that the two women had undergone "genetic testing that show that these are men".
The IOC leapt to the defence of both boxers, with president Thomas Bach saying they were born and raised as women, and have passports saying that. Neither is known to identify as transgender.
World Boxing is in talks with the International Olympic Committee to take over running the sport at the Games after the damaging gender controversy.
Lin, who went on to win the gold in her women's final, was dubbed "Taiwan's daughter" by both local media and President Lai Ching-te.
Taiwan premier Cho Jung-tai said Wednesday that the government would "actively strive to protect and secure" Lin's rights to take part in future international competitions.
